8YI8

The complex structure of SdnG with product

これはPDB形式変換不可エントリーです。

8YI8 の概要

• エントリーDOI: 10.2210/pdb8yi8/pdb
• 分子名称: Sordarin/hypoxysordarin biosynthesis cluster protein G, deoxysordaricin, (5R)-5-methyl-5-[[(1R,2R,5R)-2-methyl-5-(3-oxidanylideneprop-1-en-2-yl)cyclopentyl]methyl]-2-propan-2-yl-cyclopenta-1,3-diene-1-carboxylic acid, ... (4 entities in total)
• 機能のキーワード: diels alderase, norbornene, sordarin, product, biosynthetic protein
• 由来する生物種: Sordaria araneosa; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 66435.21

構造登録者

Zhou, J.,Zang, X.,Yi, T. (登録日: 2024-02-29, 公開日: 2025-10-22)

主引用文献

Sun, Z.,Zang, X.,Zhou, Q.,Ohashi, M.,Houk, K.N.,Zhou, J.,Tang, Y.
Iminium Catalysis in Natural Diels-Alderase.
Nat Catal, 8:218-228, 2025

PubMed Abstract: Iminium-catalyzed cycloaddition is one of the most prominent examples of organocatalysis, yet a biological counterpart has not been reported despite the wide-spread occurrence of iminium adducts in enzymes. Here, we present biochemical, structural, and computational evidence for iminium catalysis by the natural Diels-Alderase SdnG that catalyzes norbornene formation in sordarin biosynthesis. A Schiff base adduct between the ε-nitrogen of active site K127 and the aldehyde group of the enal dienophile was revealed by structural analysis and captured under catalytic conditions via borohydride reduction. This Schiff base adduct positions the substrate into near-attack conformation and decreases the transition state barrier of Diels-Alder cyclization by 8.3 kcal/mol via dienophile activation. A hydrogen bond network consisting of a catalytic triad is proposed to facilitate proton transfer required for iminium formation. This work establishes a new mode of catalysis for Diels-Alderases and points the way to the design of novel iminium based (bio)catalysts.

PubMed: 40881614
DOI: 10.1038/s41929-025-01294-w

実験手法

X-RAY DIFFRACTION (1.33 Å)